Mulder and Scully are reunited. Mulder learns about the government's part in the alien hybrid project, and about his father's part in his sister's abduction.
Call to Agriculture: Victor Klemper is a former Nazi scientist who was offered an asylum in the States. He was employed by the Syndicate as a biologist trying to create an alien human hybrid. When agents Mulder and Scully come to confront him, he is working in his greenhouse on his flowers, particularly orchids, all blooming and very beautiful.
Can't Stop the Signal: Skinner secures Mulder and Scully's safety by informing CSM that the information on the tape has been memorized by Albert Hosteen and twenty other randomly chosen Navajo, all of whom have been instructed to go public if Mulder or Scully are harmed. And Krycek promises to reveal its secrets if CSM ever goes after him.
Establishing Character Moment: Skinner changed from a shady figure who might be evil to a still shady figure who would always back Mulder and Scully up.
Evil Brit: The Well-Manicured Man, a prominent member of the Syndicate, speaks in British accent.
Faking the Dead: Krycek calls CSM to let him know the attempt on his life failed. He intends to stay off the radar, but as he has the tape, he warns CSM to never try to find him.
Gunpoint Banter: Scully and Skinner after the teaser, and Mulder joins a moment later.
Magical Native American: Mulder was brought back to life by a Native American ritual after getting gassed in a boxcar full of dead alien hybrids — although Albert Hosteen's role does turn out to be far more layered and important than just being a Font of Native Wisdom.
Man Hug: Frohike gives one to Mulder after seeing that he's alive.
Meaningful Look: Scully to Mulder at his apartment elevator, she expressing her relief that he's alive.
Mexican Standoff: Scully and Skinner's continues from "Blessing Way". Mulder joins them and resolves the issue.
Not Quite Dead: Viewers already knew it, but in this episode, the Well-Manicured Man learns and reports to the rest of the Syndicate that Mulder is alive.
Oh, Crap!: Krycek when he realizes he's in a car that's about to explode.
O.O.C. Is Serious Business: CSM is under a lot of pressure in regards to the tape, so he lets his usually cool demeanor slip when Skinner first talks about a deal.
Sadistic Choice: William Mulder was forced to choose which of his kids, Fox or Samantha, would be abducted.
Shut Up, Hannibal!: When Skinner tries to bluff about still having the tape, CSM shuts him down and proceeds to ridicule him. Skinner, however, then invites Albert Hosteen to join them and plays that card.
Those Wacky Nazis: Klemper is a former Nazi scientist. He was employed by the US government and the Syndicate after the war.